remove backwards compatibility

README.md

@@ -353,7 +353,7 @@ Under the hood, the following happens when calling `PyTorchIEPipeline.from_pretr
 </summary>
 
 ```python
-from pytorch_ie.auto import AutoTaskModule, AutoModel
+from pytorch_ie.core import AutoTaskModule, AutoModel
 from pytorch_ie.pipeline import PyTorchIEPipeline
 
 model_name_or_path = "pie/example-ner-spanclf-conll03"
@@ -375,8 +375,8 @@ ner_pipeline = PyTorchIEPipeline(model=ner_model, taskmodule=ner_taskmodule, dev
 from dataclasses import dataclass
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
 from pytorch_ie.core import AnnotationLayer, annotation_field
+from pytorch_ie.annotations import BinaryRelation, LabeledSpan
 from pytorch_ie.documents import TextDocument
 
 

examples/predict/ner_span_classification.py

@@ -1,10 +1,10 @@
 from dataclasses import dataclass
 
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerSpanClassificationModel
 from pytorch_ie.taskmodules import TransformerSpanClassificationTaskModule
 

examples/predict/re_generative.py

@@ -1,10 +1,10 @@
 from dataclasses import dataclass
 
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import BinaryRelation, LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerSeq2SeqModel
 from pytorch_ie.taskmodules import TransformerSeq2SeqTaskModule
 

examples/predict/re_text_classification.py

@@ -1,10 +1,10 @@
 from dataclasses import dataclass
 
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import BinaryRelation, LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerTextClassificationModel
 from pytorch_ie.taskmodules import TransformerRETextClassificationTaskModule
 

src/pytorch_ie/__init__.py

@@ -1,7 +1,7 @@
 # flake8: noqa
 
-from pytorch_ie.auto import AutoModel, AutoTaskModule
 from pytorch_ie.core import *
 from pytorch_ie.datamodule import PieDataModule
 from pytorch_ie.dataset import IterableTaskEncodingDataset, TaskEncodingDataset
+from pytorch_ie.model import PyTorchIEModel
 from pytorch_ie.pipeline import PyTorchIEPipeline

src/pytorch_ie/annotations.py

@@ -1,13 +1 @@
-# backward compatibility
-from pie_documents.annotations import (
-    BinaryRelation,
-    Label,
-    LabeledMultiSpan,
-    LabeledSpan,
-    MultiLabel,
-    MultiLabeledBinaryRelation,
-    MultiLabeledSpan,
-    MultiSpan,
-    NaryRelation,
-    Span,
-)
+from pie_documents.annotations import *

src/pytorch_ie/core/__init__.py

@@ -1,35 +1 @@
-import sys
-
-import pie_core
-from pie_core import taskmodule
-from pie_core.document import Annotation, AnnotationLayer, Document, annotation_field
-from pie_core.metric import DocumentMetric
-from pie_core.module_mixins import (
-    EnterDatasetDictMixin,
-    EnterDatasetMixin,
-    ExitDatasetDictMixin,
-    ExitDatasetMixin,
-    WithDocumentTypeMixin,
-)
-from pie_core.preparable import PreparableMixin
-from pie_core.statistic import DocumentStatistic
-from pie_core.taskencoding import TaskEncoding, TaskEncodingSequence
-from pie_core.taskmodule import TaskModule
-
-from pytorch_ie import model
-from pytorch_ie.dataset import IterableTaskEncodingDataset, TaskEncodingDataset
-from pytorch_ie.model import PyTorchIEModel
-
-submodules = ["document", "taskmodule", "metric", "statistic"]
-for sub in submodules:
-    module = getattr(pie_core, sub)
-    sys.modules[f"{__name__}.{sub}"] = module
-
-sys.modules[f"{__name__}.model"] = model
-
-taskmodule.TaskEncodingDataset = TaskEncodingDataset
-taskmodule.IterableTaskEncodingDataset = IterableTaskEncodingDataset
-
-# backwards compatibility
-AnnotationList = AnnotationLayer
-RequiresDocumentTypeMixin = WithDocumentTypeMixin
+from pie_core import *

src/pytorch_ie/documents.py

@@ -1,31 +1 @@
-# backwards compatibility
-from pie_documents.documents import (
-    DocumentWithLabel,
-    DocumentWithMultiLabel,
-    TextBasedDocument,
-    TextDocumentWithLabel,
-    TextDocumentWithLabeledMultiSpans,
-    TextDocumentWithLabeledMultiSpansAndBinaryRelations,
-    TextDocumentWithLabeledMultiSpansAndLabeledPartitions,
-    TextDocumentWithLabeledMultiSpansBinaryRelationsAndLabeledPartitions,
-    TextDocumentWithLabeledPartitions,
-    TextDocumentWithLabeledSpans,
-    TextDocumentWithLabeledSpansAndBinaryRelations,
-    TextDocumentWithLabeledSpansAndLabeledPartitions,
-    TextDocumentWithLabeledSpansAndSentences,
-    TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions,
-    TextDocumentWithMultiLabel,
-    TextDocumentWithSentences,
-    TextDocumentWithSpans,
-    TextDocumentWithSpansAndBinaryRelations,
-    TextDocumentWithSpansAndLabeledPartitions,
-    TextDocumentWithSpansBinaryRelationsAndLabeledPartitions,
-    TokenBasedDocument,
-    WithMetadata,
-    WithText,
-    WithTokens,
-)
-from typing_extensions import TypeAlias
-
-# backwards compatibility
-TextDocument: TypeAlias = TextBasedDocument
+from pie_documents.documents import *

src/pytorch_ie/metrics/__init__.py

@@ -1,2 +1 @@
-# backwards compatibility
-from pie_documents.metrics import ConfusionMatrix, F1Metric, SQuADF1
+from pie_documents.metrics import *

src/pytorch_ie/model.py

@@ -1,7 +1,7 @@
 from typing import Any, Dict
 
 import torch
-from pie_core import Auto, Model
+from pie_core import Model
 from pytorch_lightning import LightningModule
 
 

src/pytorch_ie/taskmodules/transformer_re_text_classification.py

@@ -25,6 +25,13 @@
 import numpy as np
 import torch
 from pie_core import AnnotationLayer, Document, TaskEncoding, TaskModule
+from pie_documents.annotations import (
+    BinaryRelation,
+    LabeledSpan,
+    MultiLabeledBinaryRelation,
+    NaryRelation,
+    Span,
+)
 from pie_documents.documents import (
     TextDocument,
     TextDocumentWithLabeledSpansAndBinaryRelations,
@@ -35,13 +42,6 @@
 from transformers.tokenization_utils_base import TruncationStrategy
 from typing_extensions import TypeAlias
 
-from pytorch_ie.annotations import (
-    BinaryRelation,
-    LabeledSpan,
-    MultiLabeledBinaryRelation,
-    NaryRelation,
-    Span,
-)
 from pytorch_ie.models.transformer_text_classification import ModelOutputType, ModelStepInputType
 from pytorch_ie.taskmodules.interface import ChangesTokenizerVocabSize
 from pytorch_ie.utils.span import get_token_slice, is_contained_in

src/pytorch_ie/utils/span.py

@@ -13,13 +13,13 @@
     Tuple,
 )
 
+from pie_documents.annotations import LabeledSpan, Span
+
 # backwards compatibility imports from pie_documents.utils.span
 from pie_documents.utils.span import have_overlap as has_overlap
 from pie_documents.utils.span import is_contained_in
 from transformers import PreTrainedTokenizer
 
-from pytorch_ie.annotations import LabeledSpan, Span
-
 # TODO: most of this should be superseded by pie_documents.utils.sequence_tagging,
 #  remove respective content
 

tests/pipeline/test_ner_span_classification.py

@@ -2,10 +2,10 @@
 
 import pytest
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerSpanClassificationModel
 from pytorch_ie.taskmodules import TransformerSpanClassificationTaskModule
 

tests/pipeline/test_re_generative.py

@@ -2,10 +2,10 @@
 
 import pytest
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import BinaryRelation, LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerSeq2SeqModel
 from pytorch_ie.taskmodules import TransformerSeq2SeqTaskModule
 

tests/pipeline/test_re_text_classification.py

@@ -3,10 +3,10 @@
 import pytest
 import torch
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import BinaryRelation, LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerTextClassificationModel
 from pytorch_ie.taskmodules import TransformerRETextClassificationTaskModule
 

tests/taskmodules/test_simple_transformer_text_classification.py

@@ -3,10 +3,10 @@
 
 import pytest
 import torch
+from pie_core import AnnotationLayer, Document, annotation_field
+from pie_documents.annotations import Label
 from transformers import BatchEncoding
 
-from pytorch_ie import AnnotationLayer, Document, annotation_field
-from pytorch_ie.annotations import Label
 from pytorch_ie.taskmodules import SimpleTransformerTextClassificationTaskModule
 from tests import _config_to_str
 

tests/taskmodules/test_transformer_seq2seq.py

@@ -3,11 +3,11 @@
 
 import pytest
 import torch
+from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import BinaryRelation, LabeledSpan
+from pie_documents.documents import TextDocument
 from transformers import BatchEncoding
 
-from pytorch_ie import AnnotationLayer, annotation_field
-from pytorch_ie.annotations import BinaryRelation, LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.taskmodules import TransformerSeq2SeqTaskModule
 
 

tests/taskmodules/test_transformer_span_classification.py

@@ -1,8 +1,8 @@
 import numpy
 import pytest
 import torch
+from pie_core import TaskModule
 
-from pytorch_ie import TaskModule
 from pytorch_ie.taskmodules import TransformerSpanClassificationTaskModule
 
 

tests/taskmodules/test_transformer_token_classification.py

@@ -4,10 +4,10 @@
 import numpy as np
 import pytest
 import torch
+from pie_core import AnnotationLayer, Document, annotation_field
+from pie_documents.annotations import LabeledSpan, Span
 from transformers import BatchEncoding
 
-from pytorch_ie import AnnotationLayer, Document, annotation_field
-from pytorch_ie.annotations import LabeledSpan, Span
 from pytorch_ie.taskmodules import TransformerTokenClassificationTaskModule
 
 

tests/test_auto.py

@@ -1,12 +1,19 @@
 from dataclasses import dataclass
 
 import pytest
-from pie_core import AnnotationLayer, AutoAnnotationPipeline, Model, TaskModule, annotation_field
+from pie_core import (
+    AnnotationLayer,
+    AutoAnnotationPipeline,
+    AutoModel,
+    AutoTaskModule,
+    Model,
+    TaskModule,
+    annotation_field,
+)
+from pie_documents.annotations import LabeledSpan
+from pie_documents.documents import TextDocument
 
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.auto import AutoModel, AutoTaskModule
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models import TransformerSpanClassificationModel
 from pytorch_ie.taskmodules import TransformerSpanClassificationTaskModule
 

tests/test_pipeline.py

@@ -4,12 +4,12 @@
 import torch
 import transformers
 from pie_core import AnnotationLayer, annotation_field
+from pie_documents.annotations import LabeledSpan
+from pie_documents.documents import TextDocument
 from transformers.modeling_outputs import BaseModelOutputWithPooling
 
 import pytorch_ie.models.modules.mlp
 from pytorch_ie import PyTorchIEPipeline
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.documents import TextDocument
 from pytorch_ie.models.transformer_span_classification import TransformerSpanClassificationModel
 from pytorch_ie.taskmodules.transformer_span_classification import (
     TransformerSpanClassificationTaskModule,

tests/utils/test_document.py

@@ -1,5 +1,6 @@
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.documents import TextDocumentWithLabeledSpans
+from pie_documents.annotations import LabeledSpan
+from pie_documents.documents import TextDocumentWithLabeledSpans
+
 from pytorch_ie.utils.document import merge_annotations_from_documents